To generate an image file of the MSA Comparator, choose the Generate image file from the Utilities menu. The Image Generation Options pop-up window will appear, as shown in Figure 1.

The available options are as follows:

• Full alignment or partial alignment: Generating an image of the full length of both alignments is the default option. If you wish to generate an image only for a specific subsection of each alignment, click on the Partial alignment radio button and then fill out the start and end positions.
• Characters per line: The default value is 100 characters per line. This value can be up to the maximum length of the longest alignment.
• Additional options available depend on the content displayed in the MSA Comparator.
  • MSA file names: Always available. Deselect if you do not want file names in the image.
  • Information content graphic: Available only if information content bar chart is visible. Deselect if you do not want it in the image.
  • SPS graphic: Available only if the SPS bar chart is visible. Deselect if you do not want it in the image.
  • Statistics: Available only if the SPS bar chart is open. Deselect if you do not want the statistics in the image. This includes the consistency score, SP score and column scores.
• Image file directory: This is the directory where the image file is saved to. A suggested directory name is generated based on the current directory. This can be changed by typing a new file name into the text box.
• Image file name: A suggested image file name is generated based on the alignment file name. This can be changed by typing a new file name into the text box.

After all options are set, click on the Generate image file button to save the alignment image in the specified location. The image file in PNG format will be created.